About This Database

Ontology

Data description

Data name

Ontology

DOI

10.18908/lsdba.nbdc01181-004.V002

Description of data contents

The ontology files that are used in MicrobeDB.jp version 2. Data file (compressed in tar.gzip) consists of some directories (see the following table).

Data file

File name :

ontology.tar.gz

File URL :

https://dbarchive.biosciencedbc.jp/data/microbedb/LATEST/ontology.tar.gz

File size :

91 MB

Simple search URL

Data acquisition method

The MPO and MCCV files were obtained from a collaborator. The NCBI Taxonomy and INSDC ontology files were obtained from the DDBJ web site. Other ontologies were developed in this project.

Data analysis method

Number of data entries

21,722,610 triples

Data detail

Data item	Description
ontology/meo/meo.ttl	An ontology for describing organismal habitats (especially focused on microbes).
ontology/meo/meo_fma_mapping.ttl	An ontology mapping files that was mapped between MEO and FMA.
ontology/msv/msv.ttl	An ontology for describing several states of sampling environment for metagenome analyses.
ontology/mdbv/mdbv.rdf	A vocabulary for describing data schema in MicrobeDB.jp version 2.
ontology/mgfo/mgfo.ttl	An ontology for describing the gene function category that is used in MBGD.
ontology/pdo/pdo.owl	An ontology for describing both human infectious diseases caused by microbes and the diseases that is related to microbial infection.
ontology/csso/csso.owl	An ontology for describing clinical signs and symptoms.
ontology/mpo/mpo.ttl	An ontology for describing microbial phenotypes.
ontology/mccv/mccv.ttl	Structured controlled vocabulary for describing meta information of microbial culture collection maintained in biological resource centers.
ontology/taxonomy/taxonomy.ttl	Modified NCBI Taxonomy ontology for describing taxonomic relationships of organisms.
ontology/insdc/nucleotide.ttl	A vocabulary for describing metadata of INSDC entries.